How do I make Python in Blender move 100 bones simutaniously?
In Blender if you want to make use of multiple CPU cores for your scripts - look into multi-processing.

Since Python's threading does not take advantage of multiple CPU's and is mainly used so multiple tasks can run without one task blocking all the others.



Note that its questionable if you even need multi-processing for this task.

Also take a look at numba (jit accelerated Python which is compatible with Blender), it can give real speedups for numeric tasks and easier to integrate then alternatives.